Line a muffin tin with 9 paper liners or use a silicone muffin tin. Set aside.
Melt 3/4 cup of the chocolate. You can use the microwave or a double boiler on the stovetop. If using the microwave, it's best to stop and stir every 30 seconds to ensure it melts evenly and doesn't burn. It should be melted after around 1 minute and 30 seconds, but it can vary with each microwave.
Pour the chocolate evenly at the bottom of each cup. Using a spoon, push some of the melted chocolate to the sides of the paper liners, about halfway to the top of each cup. This will make the sides of the cups and will ensure that the caramel doesn't pour to the sides. Place in the fridge on a flat surface and let chill for 5 minutes or until the chocolate firms up.
Meanwhile, make the cookie dough. In a small bowl, beat the butter, brown sugar and cane sugar together. Stir in the vanilla extract. Add the oat flour, almond flour and salt and stir until combined. Stir in the chocolate chips. Set aside.
Melt the remaining 1 cup of chocolate using the same method.
Remove the chocolate cups from the fridge and place a heaping tablespoon of the cookie dough in each cup. Slightly flatten the cookie dough so that it almost reaches the sides of the cups. Top every cup with more melted chocolate. Place in the fridge and let it chill for 10 minutes or until firm.
Store the cups in an airtight container in the fridge.